6KX1: SN-101 mAb

Crystal structure of SN-101 mAb in complex with MUC1 glycopeptide. Determined by X-ray diffraction at 1.77 Å resolution. Released 29 Jul 2020.

Method: X-ray diffraction
Resolution: 1.77 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 3,619
Mol. weight: 53.66 kDa
Ligands: A2G
Released: 29 Jul 2020

Explore 6KX1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6KX1 contains 18 α-helices and 45 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	9-11	3	2
β-strand	17-24	8	1
α-helix	28-30	3
β-strand	33-39	7	2
β-strand	43-50	8	2
α-helix	53-55	3
β-strand	59-61	3	2
α-helix	63-65	3
β-strand	69-74	6	1
β-strand	79-84	6	1
α-helix	89-91	3
β-strand	93-99	7	2
β-strand	104-105	2	2
β-strand	109-113	5	2
α-helix	116-118	3
β-strand	119	1	3
α-helix	120-121	2
β-strand	122-126	5	4
β-strand	137-147	11	4
β-strand	148	1	3
β-strand	153-156	4	5
α-helix	157-159	3
β-strand	161	1	5
β-strand	165-167	3	4
α-helix	168-170	3
β-strand	171-173	3	4
β-strand	176-186	11	4
α-helix	187-189	3
β-strand	196-201	6	5
α-helix	202-204	3
β-strand	206-211	6	5

Chain B: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-14	5	7
β-strand	19-25	7	6
β-strand	30	1	8
β-strand	36	1	8
β-strand	38-43	6	7
β-strand	49-54	6	7
β-strand	58-59	2	7
β-strand	67-72	6	6
β-strand	75-80	6	6
α-helix	85-87	3
β-strand	89-95	7	7
α-helix	102	1
β-strand	103-104	2	7
β-strand	108-113	6	7
β-strand	117	1	9
β-strand	120-124	5	10
α-helix	125-127	3
α-helix	128-132	5
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-156	6	11
β-strand	159-161	3	11
β-strand	165-169	5	10
α-helix	170-173	4
β-strand	179-188	10	10
α-helix	189-192	4
β-strand	197-203	7	11
α-helix	210	1
β-strand	211-216	6	11

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab Fragment-SN-101-Heavy chain	A	protein	236	Mus musculus
Fab Fragment-SN-101-Light chain	B	protein	239	Mus musculus
Synthetic MUC1 glycopepide	C	protein	16	Homo sapiens	P15941 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6KX1_1 Fab Fragment-SN-101-Heavy chain (chains A)
MDLRLSCAFIIVLLKGVQSEVNLEESGGGLVQPGGSMKLSCVASGFTFSNYWMNWVRQSP
EKGLEWVAQIRLKSDNYATHYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTGG
VFDYWGQGTTLTVSSSKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGA
LSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPRD

Sequence of entity 2 (B), FASTA

>6KX1_2 Fab Fragment-SN-101-Light chain (chains B)
MKLPVRLLVLMFWIPASSSDVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWY
LQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPP
WTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSER
QNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (C), FASTA

>6KX1_3 Synthetic MUC1 glycopepide (chains C)
XVTSAPDTRPAPGSTA

Ligands and cofactors

ID	Name	Formula	Copies
A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	C8 H15 N O6	1

Primary citation

A straightforward approach to antibodies recognising cancer specific glycopeptidic neoepitopes. Wakui, H., Tanaka, Y., Ose, T. et al. Chem Sci (2020) 11:4999-5006. DOI 10.1039/D0SC00317D

Other PDB entries of the same protein (UniProt P15941 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BSC 1.3 Å, Crystal structure of the Mucin-1 SEA domain
7V64 1.56 Å, Crystal structure of Antibody 16A in complex with MUC1 Glycopeptide(GlycoT)
6BSB 1.6 Å, Crystal structure of the Mucin-1 SEA domain, L1105M mutant, Selenium-derivative
6FZQ 1.7 Å, Crystal structure of scFv-SM3 in complex with compound 3
8S6K 1.75 Å, Crystal structure of ScFv-G2D11 complexed to a bis-Tn glycopeptide
6FZR 1.8 Å, Crystal structure of scFv-SM3 in complex with compound 2
8AXH 1.85 Å, Crystal structure of a MUC1-like glycopeptide containing the unnatural…
8S6T 1.85 Å, Crystal structure of Fab-3F1 complexed to a bis-STn glycopeptide
1SM3 1.95 Å, Crystal structure of the tumor specific antibody SM3 complex with its peptide epitope
8S6V 1.95 Å, Crystal structure of Fab-2D9 chimera complexed to a bis-Tn glycopeptide
5T6P 1.97 Å, Crystal structure of therapeutic mAB AR20.5 in complex with MUC1 peptide
6TGG 2.0 Å, scFv-1SM3 in complex with glycopeptide containing an sp2-imino sugar

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